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comparison chipseeker.xml @ 2:cb133602cd9b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit bae8cc7d7a88154b815acc3cd126010e7e965d5c
author rnateam
date Wed, 30 May 2018 06:12:27 -0400
parents 95f779f4adb7
children 535321abf9a4
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1:95f779f4adb7 2:cb133602cd9b
21 21
22 Rscript '$__tool_directory__/chipseeker.R' 22 Rscript '$__tool_directory__/chipseeker.R'
23 23
24 -i '$peaks' 24 -i '$peaks'
25 -G '$gtf' 25 -G '$gtf'
26 -u $upstream 26 -u $adv.upstream
27 -d $downstream 27 -d $adv.downstream
28 #if $flankgeneinfo: 28 #if $adv.flankgeneinfo:
29 -F $flankgeneinfo 29 -F $adv.flankgeneinfo
30 -D $flankgenedist 30 -D $adv.flankgenedist
31 #end if 31 #end if
32 -f $format 32 -f $format
33 -p $pdf 33 -p $pdf
34 ]]> 34 ]]>
35 </command> 35 </command>
36 <inputs> 36 <inputs>
37 <param name="peaks" type="data" format="bed,interval" label="Peaks file" help="A peaks file in BED format." /> 37 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
38 <conditional name="gtf_source"> 38 <conditional name="gtf_source">
39 <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source."> 39 <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source.">
40 <option value="cached" selected="true">Use a built-in GTF</option> 40 <option value="cached" selected="true">Use a built-in GTF</option>
41 <option value="history">Use a GTF from history</option> 41 <option value="history">Use a GTF from history</option>
42 </param> 42 </param>
50 </when> 50 </when>
51 <when value="history"> 51 <when value="history">
52 <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" /> 52 <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" />
53 </when> 53 </when>
54 </conditional> 54 </conditional>
55 <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." />
56 <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/>
57 <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/>
58 <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/>
59 <param name="format" type="select" label="Output Format"> 55 <param name="format" type="select" label="Output Format">
60 <option value="interval" selected="True">Interval</option> 56 <option value="interval" selected="True">Interval</option>
61 <option value="tabular">Tabular (tab-separated)</option> 57 <option value="tabular">Tabular (tab-separated)</option>
62 </param> 58 </param>
63 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" /> 59 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
64 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" /> 60 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
61
62 <section name="adv" expanded="false" title="Advanced Options">
63 <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." />
64 <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/>
65 <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/>
66 <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/>
67 </section>
65 </inputs> 68 </inputs>
66 69
67 <outputs> 70 <outputs>
68 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" > 71 <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" >
69 <change_format> 72 <change_format>
135 138
136 .. class:: infomark 139 .. class:: infomark
137 140
138 **What it does** 141 **What it does**
139 142
140 ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. See 143 ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the peak to the TSS of its nearest gene. Users can define the TSS (transcription start site) region under **Advanced Options**, by default the TSS region is defined from -3kb to +3kb. The genomic region of the peak is reported in the annotation column. Since some annotations may overlap for a peak, ChIPseeker adopts the following priority in genomic annotation:
141 the `ChIPseeker vignette`_ for more information. 144
145 * Promoter
146 * 5’ UTR
147 * 3’ UTR
148 * Exon
149 * Intron
150 * Downstream
151 * Intergenic
152
153 ChIPseeker also produces plots to help users visualise the overlaps in annotation for peaks, for example, the vennpie and upsetplot. See the `ChIPseeker vignette`_ for more information.
142 154
143 ----- 155 -----
144 156
145 **Inputs** 157 **Inputs**
146 158
147 A peaks file in BED or Interval format e.g from MACS2 or DiffBind. 159 A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind.
148 160
149 Example: 161 Example:
150 162
151 ===== ====== ====== ======== ===== ====== 163 ===== ====== ====== ======== ===== ======
152 Chrom Start End Name Score Strand 164 Chrom Start End Name Score Strand
165 **Outputs** 177 **Outputs**
166 178
167 This tool outputs 179 This tool outputs
168 180
169 * a file of annotated peaks in Interval or Tabular format 181 * a file of annotated peaks in Interval or Tabular format
170 * a PDF of plots 182 * a PDF of plots (plotAnnoPie, vennpie, upsetplot)
171 * the R script used by this tool 183 * the R script used by this tool
172 184
173 **Annotated peaks** 185 **Annotated peaks**
174 186
175 Annotation similar to below will be added to the input file. 187 Annotation similar to below will be added to the input file.